In 15.04, Nautilus' desktop name was changed from nautilus.desktop to org.gnome.Nautilus.desktop. Currently, org.gnome.Nautilus.desktop is set as NoDisplay=true and nautilus.desktop isn't, meaning that the old shortcut appears in the Unity menu instead of the new shortcut. This also means that when you remove the default Nautilus icon from favorites and re-add it by dragging the icon from the "Installed Applications" section in the Unity menu, the window matching won't work properly. You'll get a separate file icon that pops up whenever you launch it.
Expected fix: Set nautilus.desktop to NoDisplay=true and remove that line from org.gnome.Nautilus.desktop
This is related to https://bugs.launchpad.net/ubuntu/+source/unity/+bug/1436297
ProblemType: Bug
DistroRelease: Ubuntu 15.04
Package: nautilus 1:3.14.2-0ubuntu8
ProcVersionSignature: Ubuntu 3.19.0-10.10-generic 3.19.2
Uname: Linux 3.19.0-10-generic x86_64
NonfreeKernelModules: nvidia
ApportVersion: 2.17-0ubuntu1
Architecture: amd64
CurrentDesktop: Unity
Date: Wed Apr 1 09:36:33 2015
GsettingsChanges: b'org.gnome.nautilus.list-view' b'default-column-order' b"['name', 'size', 'type', 'date_modified', 'date_accessed', 'owner', 'group', 'permissions', 'mime_type', 'where']"
InstallationDate: Installed on 2015-01-20 (71 days ago)
InstallationMedia: Ubuntu 15.04 "Vivid Vervet" - Alpha amd64 (20150119)
SourcePackage: nautilus
UpgradeStatus: No upgrade log present (probably fresh install)
Confirmed, the new desktop has NoDisplay=true, so the dash lists the old name compat one